[2024-01-24 13:32:18,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,238] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,238] [INFO] DQC Reference Directory: /var/lib/cwl/stgee3db2ba-9a16-4c1d-9173-434806ca39d3/dqc_reference
[2024-01-24 13:32:19,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,732] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,732] [INFO] Running command: gunzip -c /var/lib/cwl/stgb79f185d-fb21-45db-995c-920055ce2a8d/GCF_009742725.1_ASM974272v1_genomic.fna.gz | prodigal -d GCF_009742725.1_ASM974272v1_genomic.fna/cds.fna -a GCF_009742725.1_ASM974272v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:34,775] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:34,775] [INFO] Task started: HMMsearch
[2024-01-24 13:32:34,775] [INFO] Running command: hmmsearch --tblout GCF_009742725.1_ASM974272v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee3db2ba-9a16-4c1d-9173-434806ca39d3/dqc_reference/reference_markers.hmm GCF_009742725.1_ASM974272v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:35,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:35,087] [INFO] Found 6/6 markers.
[2024-01-24 13:32:35,131] [INFO] Query marker FASTA was written to GCF_009742725.1_ASM974272v1_genomic.fna/markers.fasta
[2024-01-24 13:32:35,132] [INFO] Task started: Blastn
[2024-01-24 13:32:35,132] [INFO] Running command: blastn -query GCF_009742725.1_ASM974272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee3db2ba-9a16-4c1d-9173-434806ca39d3/dqc_reference/reference_markers.fasta -out GCF_009742725.1_ASM974272v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:36,256] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:36,261] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:36,261] [INFO] Target genome list was writen to GCF_009742725.1_ASM974272v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:36,268] [INFO] Task started: fastANI
[2024-01-24 13:32:36,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgb79f185d-fb21-45db-995c-920055ce2a8d/GCF_009742725.1_ASM974272v1_genomic.fna.gz --refList GCF_009742725.1_ASM974272v1_genomic.fna/target_genomes.txt --output GCF_009742725.1_ASM974272v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:58,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee3db2ba-9a16-4c1d-9173-434806ca39d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:58,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee3db2ba-9a16-4c1d-9173-434806ca39d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:58,884] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:58,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:58,885] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	100.0	1595	1595	95	conclusive
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	90.7924	1340	1595	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.6765	772	1595	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	79.6639	665	1595	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	79.4707	739	1595	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	79.2546	599	1595	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.1833	633	1595	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	79.1686	612	1595	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	79.1674	629	1595	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	79.1666	652	1595	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	79.1638	605	1595	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	79.1484	634	1595	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	79.0995	636	1595	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.984	589	1595	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	78.9759	614	1595	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	78.9546	603	1595	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	78.9327	629	1595	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.8765	639	1595	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.1894	510	1595	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,886] [INFO] DFAST Taxonomy check result was written to GCF_009742725.1_ASM974272v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:58,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:58,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:58,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee3db2ba-9a16-4c1d-9173-434806ca39d3/dqc_reference/checkm_data
[2024-01-24 13:32:58,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:58,938] [INFO] Task started: CheckM
[2024-01-24 13:32:58,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009742725.1_ASM974272v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009742725.1_ASM974272v1_genomic.fna/checkm_input GCF_009742725.1_ASM974272v1_genomic.fna/checkm_result
[2024-01-24 13:33:42,848] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:42,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:42,870] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:42,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:42,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009742725.1_ASM974272v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:42,871] [INFO] Task started: Blastn
[2024-01-24 13:33:42,871] [INFO] Running command: blastn -query GCF_009742725.1_ASM974272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee3db2ba-9a16-4c1d-9173-434806ca39d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_009742725.1_ASM974272v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:44,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:44,895] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:44,895] [INFO] Target genome list was writen to GCF_009742725.1_ASM974272v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:44,918] [INFO] Task started: fastANI
[2024-01-24 13:33:44,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgb79f185d-fb21-45db-995c-920055ce2a8d/GCF_009742725.1_ASM974272v1_genomic.fna.gz --refList GCF_009742725.1_ASM974272v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009742725.1_ASM974272v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:00,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:00,955] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:00,955] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009742725.1	s__Nitratireductor_D arenosus	100.0	1595	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003015025.1	s__Nitratireductor_D sp003015025	90.8981	1340	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	81.8107	968	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749525.1	s__Im94 sp009749525	79.8467	716	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Im94	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	79.6844	767	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	79.5164	574	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	79.465	739	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823835.1	s__RCIZ01 sp018823835	79.2421	602	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_000300335.1	s__Nitratireductor pacificus	79.1797	610	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	79.0761	617	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCA_017306545.1	s__Mesorhizobium sp017306545	79.0684	594	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879535.1	s__Mesorhizobium intechi	79.038	590	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896885.1	s__65-79 sp001896885	78.9918	578	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__65-79	95.0	99.97	99.97	0.97	0.97	2	-
GCA_004020645.1	s__Mesorhizobium sp004020645	78.9804	601	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_900445235.1	s__Aminobacter aminovorans	78.9757	614	1595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:00,957] [INFO] GTDB search result was written to GCF_009742725.1_ASM974272v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:00,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:00,964] [INFO] DFAST_QC result json was written to GCF_009742725.1_ASM974272v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:00,964] [INFO] DFAST_QC completed!
[2024-01-24 13:34:00,964] [INFO] Total running time: 0h1m43s